We use HetGNN (Heterogeneous Graph Neural Network) to represent node embeddings in the Breast Cancer area with the Pubmed Knowledge Graph Dataset. This includes four kinds of nodes: scientists, datasets, papers, and bioentities. Their relationships include writing, collaboration, mention, citing, and use.

We visualized scientists and datasets using K-means clustering (k=5) and T-SNE. The cluster labels are based on bioentities, abstracts, titles, TF-IDF, and chatGPT. At the bottom of this page, we list the main words of each cluster, including both bioentities-based and abstract-title-based clusters.

Operation Notes

1. Use the mouse wheel or the ‘+’ and ‘-’ buttons on the top right of the canvas to zoom in and out.
2. Hover over a node to see details.
3. Double-click to autoscale and recover default settings.
4. Click the legends to hide/show groups of nodes.
5. Other tools are located on the top right of the canvas.

Cluster 0    Cancer signaling molecules (bioentities)   Therapeutic Mechanisms (keywords)

Bioentities: 'leptin', 'NF-κB', 'ATP', 'MAPK', 'DOX', 'AKT', 'MCF7', 'ERK', 'HBXIP', 'Bax', 'MTT', 'Bcl-2', 'oxygen', 'NF-B', 'CXCR4', 'STAT3', 'p38', 'anticancer', 'curcumin', 'siRNA', 'cisplatin', 'ERα', 'CSCs', 'mTOR', 'p21', 'PEG', 'PTX'

Keywords: 'rgd', 'western', 'anticancer', 'acid', 'investigated', 'apoptosis', 'integrin', 'mechanisms', 'enhanced', 'delivery', 'inhibits', 'nfb', 'present', 'line', 'demonstrated', 'induced', 'inhibit', 'antitumor', 'nanoparticles', 'therapeutic', 'mitochondrial', 'resistance', 'addition', 'drug', 'mechanism', 'assay', 'targeting'

Cluster 1    Health and disease risk factors (bioentities)   Epidemiology and Research Methods (keywords)

Bioentities: 'overweight', 'folate', 'colorectal cancer', 'insulin', 'BCS', 'postmenopausal breast cancer', 'Tamoxifen', 'testosterone', 'vitamin D', 'MD', 'depression', 'IGF-I', 'anxiety', 'prostate cancer', 'metformin', 'obesity', 'Participants', 'estrogens', '"breast', 'diabetes'

Keywords: 'confidence', 'la', 'rr', 'research', 'embase', 'incidence', 'casecontrol', 'polymorphism', 'science', 'population', 'ratio', 'cohort', 'screening', 'diagnosis', 'will', 'physical', 'care', 'interventions', 'de', 'models', 'published', 'mortality', 'health', 'searched', 'cochrane', 'web', 'intake', 'relationship', 'associations', 'age', 'subgroup', 'les', 'databases', 'odds', 'survivors', 'conducted', 'intervention'

Cluster 2    Breast cancer genetics and biomarkers (bioentities)   Genetics and Biomarkers (keywords)

Bioentities: 'ESR1', 'CHEK2', 'CBC', 'ATM', 'BRCA1 mutation', 'PRS', 'ERBB2', 'RNA', 'c', 'AR', 'PALB2', 'breast and ovarian cancer', 'BRCA2 mutations', 'miRNA', 'Estrogen', 'single nucleotide polymorphisms', 'TP53', 'familial breast cancer', 'FGFR2'

Keywords: 'brca2', 'network', 'brca1', 'variants', 'samples', 'mirnas', 'estrogen', 'mutation', 'identify', 'dna', 'differentially', 'functional', 'her2', 'biological', 'common', 'prognosis', 'status', 'er', 'independent', 'genes', 'interaction', 'database', 'impc', 'analyses', 'mutations'

Cluster 3    Breast cancer treatments (bioentities)   Cancer Treatment and Management (keywords)

Bioentities: '5-fluorouracil', 'early breast cancer', 'diarrhea', 'fulvestrant', 'SLN', 'pertuzumab', 'bevacizumab', 'taxanes', 'hormone receptor', 'G-CSF', 'palbociclib', 'CTC', 'zoledronic acid', 'everolimus', 'ABC', 'exemestane', 'gemcitabine', 'nausea', 'anthracyclines', 'methotrexate', 'neutropenia', 'vinorelbine', 'lapatinib', 'HER2-positive breast cancer', 'Trastuzumab', 'CMF', 'taxane', 'fluorouracil'

Keywords: 'apbi', 'radiation', 'followup', 'early', 'trial', 'time', 'median', 'patient', 'lesions', 'rate', 'hr', 'trastuzumab', 'adjuvant', 'radiotherapy', 'chemotherapy', 'treated', 'lymphedema', 'recurrence', 'outcome', 'reconstruction', 'only', 'sln', 'node', 'icg', 'neoadjuvant', 'efficacy', 'axillary', 'biopsy', 'advanced', 'os', 'rates', 'plus', 'surgery', 'toxicity', 'mastectomy', 'surgical', 'sentinel', 'randomized', 'months', 'fluorescence'

Cluster 4    Tumor microenvironment and metastasis molecules (bioentities)   Tumor Metastasis and Matrix Biology (keywords)

Bioentities: 'MMPs', 'MT1-MMP', 'TIMP-2', 'uPA', 'TIMP-1', 'carcinomas', 'collagen', 'uPAR', 'steroid', 'matrix metalloproteinases', 'tumor cell', 'MMP-1', 'MMP', 'PAI-1', 'carcinoma'

Keywords: 'carcinomas', 'suggest', 'metastases', 'metalloproteinase', 'serum', 'membrane', 'type', 'metalloproteinases', 'timp2', 'inhibitors', 'stromal', 'degradation', 'bone', 'mmps', 'timp1', 'mrna', 'mmp', 'mt1mmp', 'collagen', 'tumour', 'correlated', 'extracellular', 'mmp1'